FastQC Summary

Summary statistics for all libraries
Filename Total Flagged As Poor Quality Sequence Length %GC
ERR1698341.fastq.gz 8,798,953 0 15-307 45
ERR1698342.fastq.gz 13,089,605 0 15-342 46
ERR1698343.fastq.gz 16,265,173 0 15-350 46
ERR1698344.fastq.gz 9,151,485 0 15-326 47
ERR1698345.fastq.gz 12,223,488 0 15-357 46
ERR1698346.fastq.gz 7,371,645 0 15-363 45
ERR1698347.fastq.gz 8,535,679 0 15-365 47
ERR1698348.fastq.gz 8,872,590 0 15-226 45
ERR1698349.fastq.gz 11,036,978 0 15-227 45
ERR1698350.fastq.gz 12,172,034 0 15-351 45
ERR1698351.fastq.gz 17,531,380 0 15-356 46
ERR1698352.fastq.gz 9,546,474 0 15-349 45
ERR2206799.fastq.gz 5,523,036 0 15-247 50
ERR2206800.fastq.gz 6,373,724 0 15-263 50
ERR2206801.fastq.gz 6,411,641 0 15-260 49
ERR2206802.fastq.gz 5,923,216 0 15-261 51
ERR2206803.fastq.gz 3,881,167 0 15-359 50
ERR2206804.fastq.gz 4,234,146 0 15-361 51
ERR2206805.fastq.gz 3,667,697 0 15-358 50
ERR2206806.fastq.gz 3,095,424 0 15-333 51
ERR2206807.fastq.gz 4,789,935 0 15-311 50
ERR2206808.fastq.gz 4,554,344 0 15-266 50
ERR2206809.fastq.gz 5,554,624 0 15-274 48
ERR2206810.fastq.gz 5,358,885 0 15-255 51
SRR2138286.fastq.gz 15,015,807 0 15-51 48
SRR2138287.fastq.gz 13,872,845 0 15-51 49
SRR2138288.fastq.gz 14,796,757 0 15-51 49
SRR2138289.fastq.gz 13,990,758 0 15-51 47
SRR2138290.fastq.gz 14,180,465 0 15-51 48
SRR2138291.fastq.gz 14,922,322 0 15-51 48
SRR2138292.fastq.gz 13,985,638 0 15-51 47
SRR2138293.fastq.gz 15,172,337 0 15-51 48
SRR2138294.fastq.gz 14,505,063 0 15-51 48
SRR2138295.fastq.gz 14,401,651 0 15-51 47
SRR2180293.fastq.gz 23,373,422 0 15-50 52
SRR2180294.fastq.gz 22,783,161 0 15-50 43
SRR2180295.fastq.gz 17,259,017 0 15-50 48
SRR2180296.fastq.gz 22,768,006 0 15-50 54
SRR2180297.fastq.gz 18,409,683 0 15-50 45
SRR2180298.fastq.gz 26,120,718 0 15-50 43
SRR2180299.fastq.gz 20,521,248 0 15-50 44
SRR2180300.fastq.gz 17,998,453 0 15-50 45

Read Totals

Library Sizes ranged between 3,095,424 and 26,120,718 reads.

Read totals for each library. Duplicated reads are conventionally an high overestimate at this point.

FastQC Summary

Summary of FastQC flags for each parameter

Per Base Sequence Quality

Heatmap showing mean base qualities for each library

Per Sequence Quality Scores

Heatmap showing mean sequence qualities for each library

Per Base Sequence Content

Heatmap of summed base distributions along each read

Per Sequence GC Content

GC Content Heatmap normalised to theoretical GC content in the Hsapiens Transcriptome

GC Content Distributions for all reads showing theoretical GC content from the Hsapiens Transcriptome

Sequence Length Distribution

Sequence Duplication Levels

Adapter Content

Universal Adapter Content

Overrepresented Summary

Total overrepresented sequences for each library

Total overrepresented sequences for each library

Overrepresented Sequences

## Overrepresented_sequences missing from ERR1698341.fastq.gz
## Overrepresented_sequences missing from ERR1698342.fastq.gz
## Overrepresented_sequences missing from ERR1698343.fastq.gz
## Overrepresented_sequences missing from ERR1698344.fastq.gz
## Overrepresented_sequences missing from ERR1698345.fastq.gz
## Overrepresented_sequences missing from ERR1698346.fastq.gz
## Overrepresented_sequences missing from ERR1698347.fastq.gz
## Overrepresented_sequences missing from ERR1698348.fastq.gz
## Overrepresented_sequences missing from ERR1698349.fastq.gz
## Overrepresented_sequences missing from ERR1698350.fastq.gz
## Overrepresented_sequences missing from ERR1698351.fastq.gz
## Overrepresented_sequences missing from ERR1698352.fastq.gz
## Overrepresented_sequences missing from ERR2206799.fastq.gz
## Overrepresented_sequences missing from ERR2206800.fastq.gz
## Overrepresented_sequences missing from ERR2206801.fastq.gz
## Overrepresented_sequences missing from ERR2206803.fastq.gz
## Overrepresented_sequences missing from ERR2206804.fastq.gz
## Overrepresented_sequences missing from ERR2206805.fastq.gz
## Overrepresented_sequences missing from ERR2206806.fastq.gz
## Overrepresented_sequences missing from ERR2206807.fastq.gz
## Overrepresented_sequences missing from ERR2206808.fastq.gz
## Overrepresented_sequences missing from ERR2206809.fastq.gz
## Overrepresented_sequences missing from ERR2206810.fastq.gz
## Overrepresented_sequences missing from SRR2180294.fastq.gz
## Overrepresented_sequences missing from SRR2180297.fastq.gz
## Overrepresented_sequences missing from SRR2180300.fastq.gz
Summary of the most overrepresented sequences in all files. A maximum of 30 sequences are shown
Sequence Total Present In Overall Percentage Max_Percentage Possible_Source
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 284,500 10 0% 0.223143% No Hit
CCTCACGGTACTTGTCCGCTATCGGTCTCGTGCCGGTATTTAGCCTT 241,626 10 0% 0.189642% No Hit
GGGAGTTTGACTGGGGCGGTACACCTGTCAAACGGTAACGCAGGTGTCCT 214,960 3 0% 0.435448% No Hit
GTTGGATTGTTCACCCACTAATAGGGAACGTGAGCTGGGTTTAGACCGTC 192,588 3 0% 0.464841% No Hit
CTTCGATGTCGGCTCTTCCTATCATTGTGAAGCAGAATTCACCAAGCGTT 184,681 3 0% 0.404853% No Hit
GCCCTGTTGAACTCTCTCTTCAAAGTTCTTTTCAACTTTCCCTCACGGTAC 163,176 9 0% 0.136463% No Hit
CCGGTATTTAGCCTTAGATGGAGTTTACCACCCGCTTTGGGCTGCATTCCC 156,009 9 0% 0.132140% No Hit
GCCCTCCGTACGCCACAGGTCCCTCGCCCTCGGCAGAGGGGCGGGGATTCG 132,563 8 0% 0.119030% No Hit
GTCGGCTCTTCCTATCATTGTGAAGCAGAATTCACCAAGCGTTGGATTGT 121,713 3 0% 0.228576% No Hit
GTCGCTTTTTGATCCTTCGATGTCGGCTCTTCCTATCATTGTGAAGC 120,027 3 0% 0.252178% No Hit
GGCGTACGGAAGACCCGCTCCCCGGCGCCGCTCGTGGGGGGCCCAAGTCC 113,334 3 0% 0.212091% No Hit
GCCCAGTGCTCTGAATGTCAAAGTGAAGAAATTCAATGAAGCGCGGGTAA 113,256 3 0% 0.239516% No Hit
GGGGAGTTTGACTGGGGCGGTACACCTGTCAAACGGTAACGCAGGTGTCC 91,046 3 0% 0.189801% No Hit
CCTAAGGCGAGCTCAGGGAGGACAGAAACCTCCCGT 89,058 2 0% 0.217656% No Hit
GGCGGAGATGGGCGCCGCGAGGCGTCCAGTGCGGTAACGCGACCGATCCC 79,455 2 0% 0.186990% No Hit
GTTTTAAGCAGGAGGTGTCAGAAAAGTTACCACAGGGATAACTGGCTTGT 75,156 2 0% 0.164793% No Hit
GCTGGGTTTAGACCGTCGTGAGACAGGTTAGTTTTACCCTACTGATGATG 74,286 2 0% 0.184843% No Hit
GTCCTAAGGCGAGCTCAGGGAGGACAGAAACCTCCCGT 60,972 2 0% 0.146412% No Hit
CTCTGATCGTTTTTTCACTGACCCGGTGAGGCGGGGGGGCGAGCCCCG 60,591 2 0% 0.154981% No Hit
GCTTGATCTTGATTTTCAGTACGAATACAGACCGTGAAAGCGGGGCCTC 60,591 2 0% 0.142292% No Hit
GTGGCGGCCAAGCGTTCATAGCGACGTCGCTTTTTGATCCTTCGATGTCG 60,503 2 0% 0.134417% No Hit
GCCGAAACGATCTCAACCTATTCTCAAACTTTAAATGGGTAAGAAGCCCG 58,746 2 0% 0.137913% No Hit
GCCGAAGTGGAGAAGGCTTCCATGTGAACAGCAGTTGAACATGGGTCAGT 58,511 2 0% 0.127675% No Hit
GGGTAAACGGCGGGAGTAACTATGACTCTCTTAAGGTAGCCAAATGCCTC 57,735 2 0% 0.127517% No Hit
GTTGTTGCCATGGTAATCCTGCTCAGTACGAGAGGAACCGCAGGTTC 57,362 2 0% 0.129562% No Hit
CTGATGATGTGTTGTTGCCATGGTAATCCTGCTCAGTACGAGAGGAACCG 55,708 2 0% 0.133481% No Hit
TGATGATGTGTTGTTGCCATGGTAATCCTGCTCAGTACGAGAGGAACCGC 54,436 2 0% 0.133714% No Hit
GTCTGTGATGCCCTTAGATGTCCGGGGCTGCACGCGCGCTACACTGACTG 54,226 2 0% 0.129924% No Hit
GTTGGTTTTCGGAACTGAGGCCATGATTAAGAGGGACGGCCGGGGGCATT 53,376 2 0% 0.116659% No Hit
AGCAAATATTCAAACGAGAACTTTGAAGGCCGAAGTGGAGAAGGCTTCC 51,573 2 0% 0.122922% No Hit

Session Information

R version 3.6.1 (2019-07-05)

Platform: x86_64-apple-darwin15.6.0 (64-bit)

locale: en_AU.UTF-8||en_AU.UTF-8||en_AU.UTF-8||C||en_AU.UTF-8||en_AU.UTF-8

attached base packages: parallel, stats, graphics, grDevices, utils, datasets, methods and base

other attached packages: readr(v.1.3.1), stringr(v.1.4.0), magrittr(v.1.5), scales(v.1.1.0), pander(v.0.6.3), kableExtra(v.1.1.0), dplyr(v.0.8.5), ngsReports(v.1.2.0), tibble(v.2.1.3), ggplot2(v.3.3.0) and BiocGenerics(v.0.32.0)

loaded via a namespace (and not attached): bitops(v.1.0-6), matrixStats(v.0.56.0), lubridate(v.1.7.4), webshot(v.0.5.2), RColorBrewer(v.1.1-2), httr(v.1.4.1), GenomeInfoDb(v.1.22.0), tools(v.3.6.1), R6(v.2.4.1), lazyeval(v.0.2.2), colorspace(v.1.4-1), withr(v.2.1.2), tidyselect(v.1.0.0), compiler(v.3.6.1), rvest(v.0.3.5), Biobase(v.2.46.0), Cairo(v.1.5-11), flashClust(v.1.01-2), xml2(v.1.2.5), DelayedArray(v.0.12.2), plotly(v.4.9.2), ggdendro(v.0.1-20), labeling(v.0.3), digest(v.0.6.25), Rsamtools(v.2.2.3), rmarkdown(v.2.1), XVector(v.0.26.0), jpeg(v.0.1-8.1), pkgconfig(v.2.0.3), htmltools(v.0.4.0), FactoMineR(v.2.3), highr(v.0.8), htmlwidgets(v.1.5.1), rlang(v.0.4.5), rstudioapi(v.0.11), farver(v.2.0.3), zoo(v.1.8-7), hwriter(v.1.3.2), jsonlite(v.1.6.1), crosstalk(v.1.1.0.1), BiocParallel(v.1.20.1), RCurl(v.1.98-1.1), GenomeInfoDbData(v.1.2.2), leaps(v.3.1), Matrix(v.1.2-18), Rcpp(v.1.0.4), munsell(v.0.5.0), S4Vectors(v.0.24.3), lifecycle(v.0.2.0), scatterplot3d(v.0.3-41), stringi(v.1.4.6), yaml(v.2.2.1), MASS(v.7.3-51.5), SummarizedExperiment(v.1.16.1), zlibbioc(v.1.32.0), plyr(v.1.8.6), grid(v.3.6.1), ggrepel(v.0.8.2), crayon(v.1.3.4), lattice(v.0.20-40), Biostrings(v.2.54.0), hms(v.0.5.3), knitr(v.1.28), pillar(v.1.4.3), GenomicRanges(v.1.38.0), reshape2(v.1.4.3), stats4(v.3.6.1), glue(v.1.3.2), evaluate(v.0.14), ShortRead(v.1.44.3), latticeExtra(v.0.6-29), data.table(v.1.12.8), vctrs(v.0.2.4), png(v.0.1-7), gtable(v.0.3.0), purrr(v.0.3.3), tidyr(v.1.0.2), assertthat(v.0.2.1), xfun(v.0.12), viridisLite(v.0.3.0), truncnorm(v.1.0-8), GenomicAlignments(v.1.22.1), IRanges(v.2.20.2), cluster(v.2.1.0) and ellipsis(v.0.3.0)